> comments and annotation possible against the actual text
fermats library does this and allows users to suggest papers for discussion. Most papers listed are high profile, though community participation seems low, not the best ux. Highest commented story has 62 comments on 'Ideal Money' by John Nash.
http://fermatslibrary.com/
I think comments do add value, especially for the author looking for feedback, moreso than perhaps the reader. Soundcloud has time-based comments on tracks and also general comments. Both are important. Amazon's book reviews also work well.
Another important aspect of research is references/bibliography and it would be great to have an in-text access to a reference. eg a popup that can reveal the exact quote or piece of text that a paper is referring to. Doing reference cross-checks is something that can be very tedious but could be great at locating additional and interesting material for the reader.
Surely this use-case has been addressed in current journal UX..
fermats library does this and allows users to suggest papers for discussion. Most papers listed are high profile, though community participation seems low, not the best ux. Highest commented story has 62 comments on 'Ideal Money' by John Nash. http://fermatslibrary.com/